Stefano Iantorno | 8 Mar 22:41 2014

Help with sliding window analysis on GRanges object


I am trying to conduct a sliding window analysis on a GRanges object. My
ranges are a list of 60272 single nucleotide positions representing high
confidence SNPs stored as IRanges object. I would like to retrieve the
list of GRanges row IDs for each  500bp window in the genome
(overlapping windows).

All the documentation I could find on sliding window functions such as
runsum, runmean, etc are all for Rle objects. 

Any idea where to start from? I can't figure out a way to pick windows
in the IRanges object across intervals, since each interval is
represented by a start and end position (same genomic position since
it's a single nucleotide long).

Any help will be greatly appreciated.


-          Stefano


 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

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